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Bonferroni p-value correction in R

Recently, I had a project where I calculated many p-values and discovered that this method didn’t correct for multiple comparisons. In order to adjust for them, I searched for a way in R and realized that implementing a multiple testing adjustment is easier than I thought/remembered.

The method I’ll cover a simple correction method called the Bonferroni correction,

Simply speaking, each statistical test you make has a chance of erroneous inference because the number of rare events increases. As the these rare events increases the chance of incorrectly rejecting the null hypothesis increases.

This chance of incorrectly rejecting the null hypothesis is what we want to correct for.

You can read more here. But now let’s get to the code1.

# Reproducibility
set.seed(123)

# Create sample data of 50 data points and the p-value from zero
x <- rnorm(50, mean = c(rep(0, 25), rep(3, 25)))
p <- 2*pnorm(sort(-abs(x)))

# See unadjusted p-values and adjusted p-values
round(p, 3)
#  [1] 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.001 0.002
# [13] 0.003 0.004 0.005 0.007 0.007 0.009 0.009 0.011 0.021 0.049 0.061 0.063
# [25] 0.074 0.083 0.086 0.119 0.189 0.206 0.221 0.286 0.305 0.466 0.483 0.492
# [37] 0.532 0.575 0.578 0.619 0.636 0.645 0.656 0.689 0.719 0.818 0.827 0.897
# [49] 0.912 0.944

round(p.adjust(p, "bonferroni"), 3)
#  [1] 0.000 0.001 0.001 0.005 0.005 0.006 0.007 0.008 0.011 0.019 0.031 0.081
# [13] 0.165 0.177 0.262 0.342 0.353 0.440 0.470 0.565 1.000 1.000 1.000 1.000
# [25] 1.000 1.000 1.000 1.000 1.000 1.000 1.000 1.000 1.000 1.000 1.000 1.000
# [37] 1.000 1.000 1.000 1.000 1.000 1.000 1.000 1.000 1.000 1.000 1.000 1.000
# [49] 1.000 1.000

Above, we’ve generated a random normal distribution of numbers with varying means. Next, we calculate it’s p-value, with the null hypothesis being the mean is zero.

The function to adjust p-values is intuitively called p.adjust() and it apart of base R’s built-in stats package. This function takes in a vector of p-values and adjusts it accordingly.

The Bonferroni method is a conservative measure, meaning it treats all the tests as equals. In this case, it divides the significance level () by the number of comparisons ().

Adjusting the p-values themselves here requires we instead multiply the p-value by the number of comparisons, rather than dividing.

Alternative controlling procedures are more sophisticated in its correction.

Just a proof that this is how the function works, we can manually adjust these p-values to arrive at the same values.

# If the p-value goes greater than 1, just set to one, otherwise multiply the
# p-value
auto <- round(p.adjust(p, "bonferroni"), 3)
manually <- round(ifelse(p*length(p) > 1, 1, p*length(p)), 3)

identical(auto, manually)
# [1] TRUE

Here’s the help page for the p.adjust() function for more information.

  1. In looking into rnorm(), I found out you can precisely specify the mean of each random number generated. In this case, the first 25 numbers have a mean of 0, and the second 25 numbers have a mean of 3.